Is DNAH11 p.Arg20Ser (c.58C>A) pathogenic?

DNAH11 p.Arg20Ser (c.58C>A) is classified Conflicting classifications of pathogenicity in DNAH11 (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2026-02-02). AlphaMissense: likely benign (0.1393); Low-frequency (popmax 2.51%, amr); Associated with primary ciliary dyskinesia.

What condition is associated with DNAH11 p.Arg20Ser (c.58C>A)?

DNAH11 p.Arg20Ser (c.58C>A) is associated with primary ciliary dyskinesia, primary ciliary dyskinesia 7 (ClinVar).

How common is DNAH11 p.Arg20Ser (c.58C>A) in the general population?

DNAH11 p.Arg20Ser (c.58C>A) is low-frequency (popmax 2.51%, amr) (gnomAD).

How is Primary ciliary dyskinesia inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about DNAH11 p.Arg20Ser (c.58C>A)?

AlphaMissense predicts likely benign (score 0.1393) — an in-silico prediction, not a clinical call.

DNAH11 p.Arg20Ser

c.58C>A · rs72655967 · VCV218583

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.1393 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.51%, amr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
AlphaMissense	0.1393	likely benign
REVEL	0.113	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.9	GERP -1.5
Regional constraint	o/e 1.28	unconstrained · MANE · 358 kb · p 1.1e-96 · regional, not allelic
Overall
CADD	9.545	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.51% Admixed American · 1,280/50,964 alleles

Filtering AF 2.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.35%

Overall 0.0973% 1,508/1,549,134 alleles · low-frequency exomes 1,223/1,396,824 · genomes 285/152,310 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	2.51%	40
East Asian	0.299%	335
Remaining individualsnot grpmax-eligible	0.0883%	1,132
African / African-American	0.0438%	2,285
European (non-Finnish)	0.00174%	57,307
South Asian	0.00119%	83,984

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DNAH11
Protein: p.Arg20Ser
Coding: c.58C>A
MANE Select: NM_001277115
dbSNP: rs72655967
Type: single nucleotide variant
Location: chr7:21543303 (GRCh38)
Gene constraint: LOEUF 0.912 · pLI <0.01 (gnomAD)
Residue 20: the 'stem' region

Full DNAH11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: primary ciliary dyskinesia 7

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

Similar variants

DNAH11 p.Arg20Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
DNAH11 c.10166-1G>C Likely pathogenic ★★ same condition
DNAH11 c.10569-2A>G Likely pathogenic ★★ same condition
DNAH11 c.10691+1G>T Pathogenic/Likely pathogenic ★★ same condition
DNAH11 c.10896+1G>T Pathogenic/Likely pathogenic ★★ same condition
DNAH11 c.11203-1G>C Pathogenic/Likely pathogenic ★★ same condition
DNAH11 c.11839+1G>A Pathogenic/Likely pathogenic ★★ same condition
DNAH11 c.11968-1G>C Pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dnah11-p-arg20ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown